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Showing NP-Card for Methyl bisnorbiotinyl ketone (NP0087210)

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Record Information
Version2.0
Created at2022-05-11 16:43:09 UTC
Updated at2022-05-11 16:43:09 UTC
NP-MRD IDNP0087210
Secondary Accession NumbersNone
Natural Product Identification
Common NameMethyl bisnorbiotinyl ketone
DescriptionMethyl bisnorbiotinyl ketone belongs to the class of organic compounds known as thienoimidazolidines. These are heterocyclic compounds containing a thiophene ring fused to an imidazolidine ring. Thiophene is 5-membered ring consisting of four carbon atoms and one sulfur atom. Imidazolidine is 5-membered saturated ring of three carbon atoms, and two nitrogen centers at the 1- and 3-positions. Methyl bisnorbiotinyl ketone was first documented in 1997 (PMID: 9022537). Methyl bisnorbiotinyl ketone is an extremely weak basic (essentially neutral) compound (based on its pKa) (PMID: 9039841).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0087210 (Methyl bisnorbiotinyl ketone)

Biotin sulfone.mol
  Mrv0541 02231219592D          

 16 17  0  0  0  0            999 V2000
   -2.0975    0.6706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2266   -0.1443    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4915   -0.5188    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9081    0.0645    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2827    0.7996    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1170   -1.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1731   -0.3100    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3021   -1.1249    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6809    1.2539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5620    0.0645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2539   -0.3848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9890   -0.0103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6809   -0.4596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9890    0.8147    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3248    0.6479    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0749   -1.1022    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  7  8  1  0  0  0  0
  6  8  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  1  9  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
  7 10  1  6  0  0  0
  4 15  1  1  0  0  0
  3 16  1  1  0  0  0
M  END
Download

3D MOL for NP0087210 (Methyl bisnorbiotinyl ketone)

     RDKit          3D

 28 29  0  0  0  0  0  0  0  0999 V2000
    4.3085    0.8993    0.2141 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2665    0.0858   -0.4642 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4419   -0.4323   -1.5408 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9530   -0.1012    0.2048 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0189   -0.9547   -0.6291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2625   -1.0820    0.1238 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4948   -2.0959   -0.7725 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9773   -1.2057   -0.1407 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3576   -0.3291    0.9022 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0917    0.9470    0.8546 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7223    1.4609   -0.4361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3663    2.3626   -1.0537 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5253    0.7837   -0.8815 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0267    0.1573    0.3176 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1327    1.9677   -0.0290 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2993    0.7157    1.3130 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3311    0.6530   -0.1379 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0852   -0.5657    1.1936 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4626    0.8986    0.3773 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9282   -0.4795   -1.6047 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5014   -1.9452   -0.7245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1198   -1.5781    1.1047 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3419   -0.5914   -0.9900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7023   -1.9083    0.2560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2732   -0.7411    1.8898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7047    1.3452    1.5738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1897    0.8048   -1.8550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5731    0.9287    0.9342 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  2  1  0
  2  1  1  0
  2  3  2  0
  6 14  1  0
 14 13  1  0
 13 11  1  0
 11 12  2  0
 11 10  1  0
 14  9  1  0
 10  9  1  0
  9 25  1  1
  8 23  1  0
  8 24  1  0
  6 22  1  1
  5 20  1  0
  5 21  1  0
  4 18  1  0
  4 19  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
 14 28  1  1
 13 27  1  0
 10 26  1  0
M  END
Download

3D SDF for NP0087210 (Methyl bisnorbiotinyl ketone)

Biotin sulfone.mol
  Mrv0541 02231219592D          

 16 17  0  0  0  0            999 V2000
   -2.0975    0.6706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2266   -0.1443    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4915   -0.5188    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9081    0.0645    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2827    0.7996    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1170   -1.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1731   -0.3100    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3021   -1.1249    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6809    1.2539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5620    0.0645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2539   -0.3848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9890   -0.0103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6809   -0.4596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9890    0.8147    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3248    0.6479    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0749   -1.1022    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  7  8  1  0  0  0  0
  6  8  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  1  9  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
  7 10  1  6  0  0  0
  4 15  1  1  0  0  0
  3 16  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0087210

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12CS[C@@H](CCC(C)=O)[C@@]1([H])NC(=O)N2

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N2O2S/c1-5(12)2-3-7-8-6(4-14-7)10-9(13)11-8/h6-8H,2-4H2,1H3,(H2,10,11,13)/t6-,7-,8-/m0/s1

> <INCHI_KEY>
ITHUGYGPPSVHRH-FXQIFTODSA-N

> <FORMULA>
C9H14N2O2S

> <MOLECULAR_WEIGHT>
214.285

> <EXACT_MASS>
214.077598392

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
21.507729121835144

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3aS,4S,6aR)-4-(3-oxobutyl)-hexahydro-1H-thieno[3,4-d]imidazolidin-2-one

> <ALOGPS_LOGP>
-0.08

> <JCHEM_LOGP>
-0.2400881593333334

> <ALOGPS_LOGS>
-2.21

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.40742292995758

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.515589593145577

> <JCHEM_PKA_STRONGEST_BASIC>
-1.8636462795618347

> <JCHEM_POLAR_SURFACE_AREA>
58.199999999999996

> <JCHEM_REFRACTIVITY>
54.400000000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.32e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3aS,4S,6aR)-4-(3-oxobutyl)-hexahydrothieno[3,4-d]imidazolidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0087210 (Methyl bisnorbiotinyl ketone)

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PDB for NP0087210 (Methyl bisnorbiotinyl ketone)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Biotin sulfone.mol                                
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      -3.915   1.252   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -4.156  -0.269   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -2.784  -0.968   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.695   0.120   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -2.394   1.493   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -2.085  -2.341   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.323  -0.579   0.000  0.00  0.00           C+0
HETATM    8  S   UNK     0      -0.564  -2.100   0.000  0.00  0.00           S+0
HETATM    9  O   UNK     0      -5.004   2.341   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       1.049   0.120   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.341  -0.718   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.713  -0.019   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.004  -0.858   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       3.713   1.521   0.000  0.00  0.00           O+0
HETATM   15  H   UNK     0      -0.606   1.209   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0      -3.873  -2.057   0.000  0.00  0.00           H+0
CONECT    1    2    5    9                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    6   16                                             
CONECT    4    3    5    7   15                                             
CONECT    5    4    1                                                       
CONECT    6    8    3                                                       
CONECT    7    8    4   10                                                  
CONECT    8    7    6                                                       
CONECT    9    1                                                            
CONECT   10   11    7                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15    4                                                            
CONECT   16    3                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

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3D PDB for NP0087210 (Methyl bisnorbiotinyl ketone)
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SMILES for NP0087210 (Methyl bisnorbiotinyl ketone)
[H][C@]12CS[C@@H](CCC(C)=O)[C@@]1([H])NC(=O)N2
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INCHI for NP0087210 (Methyl bisnorbiotinyl ketone)
InChI=1S/C9H14N2O2S/c1-5(12)2-3-7-8-6(4-14-7)10-9(13)11-8/h6-8H,2-4H2,1H3,(H2,10,11,13)/t6-,7-,8-/m0/s1
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Synonyms
ValueSource
Bisnorbiotin methyl ketoneHMDB
[3AS-(3aa,4b,6aa)]-tetrahydro-4-(3-oxobutyl)-1H-thieno[3,4-D]imidazol-2(3H)-oneHMDB
Chemical FormulaC9H14N2O2S
Average Mass214.2850 Da
Monoisotopic Mass214.07760 Da
IUPAC Name(3aS,4S,6aR)-4-(3-oxobutyl)-hexahydro-1H-thieno[3,4-d]imidazolidin-2-one
Traditional Name(3aS,4S,6aR)-4-(3-oxobutyl)-hexahydrothieno[3,4-d]imidazolidin-2-one
CAS Registry NumberNot Available
SMILES
[H][C@]12CS[C@@H](CCC(C)=O)[C@@]1([H])NC(=O)N2
InChI Identifier
InChI=1S/C9H14N2O2S/c1-5(12)2-3-7-8-6(4-14-7)10-9(13)11-8/h6-8H,2-4H2,1H3,(H2,10,11,13)/t6-,7-,8-/m0/s1
InChI KeyITHUGYGPPSVHRH-FXQIFTODSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thienoimidazolidines. These are heterocyclic compounds containing a thiophene ring fused to an imidazolidine ring. Thiophene is 5-membered ring consisting of four carbon atoms and one sulfur atom. Imidazolidine is 5-membered saturated ring of three carbon atoms, and two nitrogen centers at the 1- and 3-positions.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassThienoimidazolidines  
Sub ClassNot Available
Direct ParentThienoimidazolidines  
Alternative Parents
Substituents
  • Thienoimidazolidine
    • 

  • Imidazolidinone
    • 

  • Imidazolidine
    • 

  • Thiolane
    • 

  • Thiophene
    • 

  • Ketone
    • 

  • Carbonic acid derivative
    • 

  • Urea
    • 

  • Thioether
    • 

  • Dialkylthioether
    • 

  • Azacycle
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.08ALOGPS
logP-0.24ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)13.52ChemAxon
pKa (Strongest Basic)-1.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area58.2 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity54.4 m³·mol⁻¹ChemAxon
Polarizability21.51 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0004822  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023430  
KNApSAcK IDNot Available
Chemspider ID13628421  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID7084  
PubChem Compound21252323  
PDB IDNot Available
ChEBI ID89480  
Good Scents IDNot Available
References
General References
  1. Zempleni J, McCormick DB, Mock DM: Identification of biotin sulfone, bisnorbiotin methyl ketone, and tetranorbiotin-l-sulfoxide in human urine. Am J Clin Nutr. 1997 Feb;65(2):508-11. [PubMed:9022537  ] 
  2. Mock DM, Wang KS, Kearns GL: The pig is an appropriate model for human biotin catabolism as judged by the urinary metabolite profile of radioisotope-labeled biotin. J Nutr. 1997 Feb;127(2):365-9. doi: 10.1093/jn/127.2.365. [PubMed:9039841  ]